Long Read Sequencing Report

Created on 2024-06-30 with Bamboo v0.1.0



FastQ Analysis Report

Input FASTQ Path: /data4/chs/00.software/Bamboo-main/test/data/ecoli_hifi.reads.fastq.gz

Output Path: /data4/chs/00.software/test_bamboo_fastqtobam4/sequence

Reference-Free QC

1. FastQ QC Summary

Metric Value
Total_reads 250
Total_bases 3709410
Average_gc_content 50.92
Average_read_quality -1.90
Read N50 14783
Average_read_length 14837.64
<1kb read proportion 0.00
<2kb read proportion 0.00
<5kb read proportion 0.00
<10kb read proportion 0.00
<50kb read proportion 1.00

2. Sequence Length

length_distribution.png
cumulative_plot.png

3. Sequencing Quality

3.1 Per-read quality distribution

quality_distribution.png

3.2 Base quality along read relative position

quality_distribution_across_read.png

3.3 Base quality in 5'/3' end

read_head_quality.png
read_tail_quality.png

4. Length vs Quality

read_len_vs_q.png

5. Read Content Metrics

5.1 Read GC%

reads_gc.png

5.2 Base content in 5'/3' end

head_base_content.png
tail_base_content.png

5.3 Homo Distribution in 3' end

homopolymer_length_distribution.png
homopolymer_event_distribution.png

5.4 Heteropolymer Distribution in 3' end

heteropolymer_length_distribution.png
heteropolymer_event_distribution.png

5.5 Homo/Heteropolymer occurrences

homopolymer_frequency_per10kb.png
heteropolymer_frequency_per10kb.png


Reference-based QC

Input BAM Path: /data4/chs/00.software/test_bamboo_fastqtobam4/alignment/sample.temp.bam

Reference Genome Path: /data4/chs/00.software/Bamboo-main/test/data/ecoli.reference.fasta.gz

Output Path: /data4/chs/00.software/test_bamboo_fastqtobam4/alignment

Reference-based QC

1. Bam QC Summary

Total_reads311
Unmapped_reads0
Secondary_alignment_reads0
Supplementary_alignment_reads61
Forward_strand_reads148
Reverse_strand_reads163
Mismatch_count29258
Mismatch_error_rate(percent)0.83
Deletion_count86659
Deletion_error_rate(percent)2.47
Insertion_count36444
Insertion_error_rate(percent)1.04
Overall_error_count152361
Overall_error_error_rate(percent)4.34

2. Coverage and bias

2.1 Coverage along chromosomes

test_bamboo_fastqtobam4/alignment/error_and_bias/whole_genome_coverage.png

2.2 Coverage fraction

test_bamboo_fastqtobam4/alignment/error_and_bias/Genome_Fraction_Coverage.png

2.3 GC% vs. Cov-normalized

test_bamboo_fastqtobam4/alignment/error_and_bias/gc_vs_coverage.png

3. Sequencing accuracy/error levels

3.1 Read acc% distribution

test_bamboo_fastqtobam4/alignment/error_and_bias/per_read_error.png

3.2 Error Rate Distribution

test_bamboo_fastqtobam4/alignment/error_and_bias/overall_error_rate.png
test_bamboo_fastqtobam4/alignment/error_and_bias/substitution_error_profile.png
test_bamboo_fastqtobam4/alignment/error_and_bias/indel.png

3.3 Relationship between read quality and error rate

test_bamboo_fastqtobam4/alignment/error_and_bias/read_quality_vs_identity.png

4. Low complexity regions

4.1 Homo length vs. expansion/contraction rate

test_bamboo_fastqtobam4/alignment/homopolymer_and_dimer/homo_error_overall.png
test_bamboo_fastqtobam4/alignment/homopolymer_and_dimer/homo_error_subplot.png
test_bamboo_fastqtobam4/alignment/homopolymer_and_dimer/homo_heatmap_overall.png
test_bamboo_fastqtobam4/alignment/homopolymer_and_dimer/homo_heatmaps_subplot.png

4.2 Heteropolymer length vs. expansion/contraction rate

test_bamboo_fastqtobam4/alignment/homopolymer_and_dimer/dimer_error_overall.png
test_bamboo_fastqtobam4/alignment/homopolymer_and_dimer/dimer_error_subplot.png
test_bamboo_fastqtobam4/alignment/homopolymer_and_dimer/dimer_heatmap_overall.png
test_bamboo_fastqtobam4/alignment/homopolymer_and_dimer/dimer_heatmaps_subplot.png